Dec 23, 2014
Export Datasets from InSilicoDB to GenePattern
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Export Datasets from InSilicoDB to GenePattern
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"Solving Problems", part II
Regarding this post, thanks to some feedback from some of the GenePattern team, both scripts are both available as GenePattern Modules at the GParc! Consider yourself integrated.
TCGA.Merge RXCtoGCT
I LIKE SOLVING PROBLEMS
Had a labmate come by and ask for help with TCGA Level 3 expression data. Its distributed as one file per sample, which when you have several HUNDRED specimens, isn't really the kind of thing you can or want to re-format by hand if you want to make comparisons across samples.
"How Hard Can it Be?!" I said. Oh when will I learn...
Two days and several infinite loops later, I present two dainty perl scripts for:
a) Take n many sample files and corral them into one flat file, probes x samples. (TCGA Merge)
b) Take a tab delimited text file with x probes and y samples and turn it into a GenePattern-friendly .gct file. (RXC to GCT)
Comes with no warranty, yadda, yadda. Would love to know if this is useful for anyone else, and remember, WATCH YOUR LINE ENDINGS!